def test_valid_sample_name_should_not_return_error(self):
# Given
sample_attributes = {
'scientific_name': 'Severe acute respiratory syndrome coronavirus 2'
}
self.taxonomy_validator.ena_taxonomy.validate_scientific_name = MagicMock(return_value=self.valid_sarscov2)
sample = Entity('sample', 'sample1', sample_attributes)
# When
self.taxonomy_validator.validate_entity(sample)
# Then
self.assertFalse(sample.has_errors())
self.assertDictEqual({}, sample.get_errors())
def test_valid_sample_tax_id_should_not_return_error(self):
# Given
sample_attributes = {
'tax_id': '2697049'
}
self.taxonomy_validator.ena_taxonomy.validate_tax_id = MagicMock(return_value=self.valid_sarscov2)
sample = Entity('sample', 'sample1', sample_attributes)
# When
self.taxonomy_validator.validate_entity(sample)
# Then
self.assertFalse(sample.has_errors())
self.assertDictEqual({}, sample.get_errors())
def test_invalid_name_should_return_error(self):
sample_attributes = {'scientific_name': 'Lorem Ipsum'}
error = 'Not valid scientific_name: Lorem Ipsum.'
expected_error = {
'scientific_name': [error]
}
self.taxonomy_validator.ena_taxonomy.validate_scientific_name = MagicMock(return_value={'error': error})
sample = Entity('sample', 'sample1', sample_attributes)
# When
self.taxonomy_validator.validate_entity(sample)
# Then
self.assertTrue(sample.has_errors())
self.assertDictEqual(expected_error, sample.get_errors())
def test_invalid_tax_id_should_return_error(self):
# Given
sample_attributes = {'tax_id': '999999999999'}
error = 'Not valid tax_id: 999999999999.'
expected_error = {
'tax_id': [error]
}
self.taxonomy_validator.ena_taxonomy.validate_tax_id = MagicMock(return_value={'error': error})
sample = Entity('sample', 'sample1', sample_attributes)
# When
self.taxonomy_validator.validate_entity(sample)
# Then
self.assertTrue(sample.has_errors())
self.assertDictEqual(expected_error, sample.get_errors())
def test_inconsistent_sample_should_return_error(self):
# Given
sample_attributes = {
'scientific_name': 'Severe acute respiratory syndrome coronavirus 2',
'tax_id': '9606'
}
self.taxonomy_validator.ena_taxonomy.validate_scientific_name = MagicMock(return_value=self.valid_sarscov2)
self.taxonomy_validator.ena_taxonomy.validate_tax_id = MagicMock(return_value=self.valid_human)
consistent_error = 'Information is not consistent between taxId: 9606 and scientificName: Severe acute respiratory syndrome coronavirus 2'
expected_errors = {
'scientific_name': [consistent_error],
'tax_id': [consistent_error]
}
sample = Entity('sample', 'sample1', sample_attributes)
# When
self.taxonomy_validator.validate_entity(sample)
# Then
self.assertTrue(sample.has_errors())
self.assertDictEqual(expected_errors, sample.get_errors())
def test_invalid_sample_name_should_return_error(self):
# Given
sample_attributes = {
'scientific_name': 'Lorem Ipsum',
'tax_id': '2697049'
}
error = 'Not valid scientific_name: Lorem Ipsum.'
consistent_error = 'Information is not consistent between taxId: 2697049 and scientificName: Lorem Ipsum'
expected_errors = {
'scientific_name': [error, consistent_error],
'tax_id': [consistent_error]
}
self.taxonomy_validator.ena_taxonomy.validate_scientific_name = MagicMock(return_value={'error': error})
self.taxonomy_validator.ena_taxonomy.validate_tax_id = MagicMock(return_value=self.valid_sarscov2)
sample = Entity('sample', 'sample1', sample_attributes)
# When
self.taxonomy_validator.validate_entity(sample)
# Then
self.assertTrue(sample.has_errors())
self.assertDictEqual(expected_errors, sample.get_errors())
